[2] | 1 | <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1">
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| 2 | <description>Alignment coverage information</description>
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| 3 | <command interpreter="python">
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| 4 | maf_stats.py
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| 5 | #if $maf_source_type.maf_source == "user":
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| 6 | $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
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| 7 | #else:
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| 8 | $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
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| 9 | #end if
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| 10 | ${GALAXY_DATA_INDEX_DIR} |
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| 11 | #if $maf_source_type.maf_source == "user": |
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| 12 | $input2.metadata.maf_index |
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| 13 | #end if
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| 14 | </command>
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| 15 | <inputs>
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| 16 | <param format="interval" name="input1" label="Interval File" type="data">
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| 17 | <validator type="unspecified_build" />
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| 18 | </param>
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| 19 | <conditional name="maf_source_type">
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| 20 | <param name="maf_source" type="select" label="MAF Source">
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| 21 | <option value="cached" selected="true">Locally Cached Alignments</option>
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| 22 | <option value="user">Alignments in Your History</option>
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| 23 | </param>
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| 24 | <when value="user">
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| 25 | <param format="maf" name="input2" label="MAF File" type="data">
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| 26 | <options>
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| 27 | <filter type="data_meta" ref="input1" key="dbkey" />
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| 28 | </options>
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| 29 | <validator type="dataset_ok_validator" />
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| 30 | </param>
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| 31 | </when>
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| 32 | <when value="cached">
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| 33 | <param name="mafType" type="select" label="MAF Type">
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| 34 | <options from_file="maf_index.loc">
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| 35 | <column name="name" index="0"/>
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| 36 | <column name="value" index="1"/>
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| 37 | <column name="dbkey" index="2"/>
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| 38 | <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
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| 39 | <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
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| 40 | </options>
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| 41 | </param>
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| 42 | </when>
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| 43 | </conditional>
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| 44 | <param name="summary" type="select" label="Type of Output">
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| 45 | <option value="false" selected="true">Coverage by Region</option>
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| 46 | <option value="true">Summarize Coverage</option>
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| 47 | </param>
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| 48 | </inputs>
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| 49 | <outputs>
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| 50 | <data format="interval" name="out_file1" metadata_source="input1">
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| 51 | <change_format>
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| 52 | <when input="summary" value="true" format="tabular" />
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| 53 | </change_format>
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| 54 | </data>
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| 55 | </outputs>
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| 56 | <requirements>
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| 57 | <requirement type="python-module">numpy</requirement>
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| 58 | </requirements>
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| 59 | <tests>
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| 60 | <test>
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| 61 | <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
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| 62 | <param name="maf_source" value="cached"/>
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| 63 | <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
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| 64 | <output name="out_file1" file="maf_stats_interval_out.dat"/>
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| 65 | <param name="summary" value="false"/>
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| 66 | </test> |
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| 67 | <test>
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| 68 | <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
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| 69 | <param name="maf_source" value="cached"/>
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| 70 | <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
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| 71 | <output name="out_file1" file="maf_stats_summary_out.dat"/>
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| 72 | <param name="summary" value="true"/>
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| 73 | </test>
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| 74 | </tests>
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| 75 | <help>
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| 76 |
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| 77 | **What it does**
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| 78 |
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| 79 | This tool takes a MAF file and an interval file and relates coverage information by interval for each species.
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| 80 | If a column does not exist in the reference genome, it is not included in the output.
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| 81 |
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| 82 | Consider the interval: "chrX 1000 1100 myInterval"
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| 83 | Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:
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| 84 |
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| 85 | chrX 1000 1100 myInterval H XXX YYY
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| 86 |
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| 87 | chrX 1000 1100 myInterval M XXX YYY
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| 88 |
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| 89 | chrX 1000 1100 myInterval R XXX YYY
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| 90 |
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| 91 |
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| 92 | where XXX and YYY are:
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| 93 |
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| 94 | XXX = number of nucleotides
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| 95 |
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| 96 | YYY = number of gaps
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| 97 |
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| 98 | ----
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| 99 |
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| 100 | Alternatively, you can request only summary information for a set of intervals:
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| 101 |
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| 102 | ======== =========== ========
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| 103 | #species nucleotides coverage
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| 104 | ======== =========== ========
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| 105 | hg18 30639 0.2372
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| 106 | rheMac2 7524 0.0582
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| 107 | panTro2 30390 0.2353
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| 108 | ======== =========== ========
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| 109 |
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| 110 | where **coverage** is the number of nucleotides divided by the total length of the provided intervals.
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| 111 | </help>
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| 112 | </tool>
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